Life constantly arises from “nonliving matter”

Creationists often argue that scientists’ lack of knowledge about how the first cell arose is evidence that life could not have arisen “spontaneously from nonliving matter.” There are numerous problems with this argument, some of which I have dealt with before. For example, it is entirely an argument from ignorance fallacy (details here). Further, although it is often used as an argument “against evolution” it is actually an entirely separate concept from the theory of evolution, and the two theories do not rely on each other (details here). In this post, however, I want to focus on a different aspect of this argument. Namely, the fact that it isn’t actually true. Life arises spontaneously from “nonliving matter” all the time. Creationists simply frame the argument in a deceptive way that ignores the chemical nature of living organisms. Every time an organism reproduces, life is arising from nonliving matter. Now, creationists will, of course, object to that claim because that new life came from the reproduction of another living organism, but that is actually entirely irrelevant. As I will explain in detail, life itself is simply a product of highly complex chemistry, and the process of reproduction consists entirely of chemical reactions among nonliving atoms. The living organism simply provides the environment in which that chemistry can take place.

Definition of “spontaneous”

The first thing that we need to talk about in this discussion is the definition of “spontaneous.” In chemistry, spontaneous has a specific meaning. It gets a bit technical with concepts like entropy, but the easiest way to understand it is that a spontaneous reaction is exothermic (meaning that it releases energy into the environment), whereas a nonspontaneous reaction is endothermic (meaning that it requires energy from the environment). This is an oversimplification, but that is not really important for this post.

The definition used by chemists is not, however, generally what creationists mean when they talk about a “spontaneous” formation of life. Rather, they seem to mean simply an event that could happen naturally without conscious intervention. Although not technical, we can use this definition, but I think we need to carefully clarify it at the outset. By this definition, given the right environmental conditions (including temperature, enzymes, etc.) any chemical reaction is spontaneous. Imagine, for example, that I take a small salt crystal, and drop it into water. The salt will dissolve because the positive sodium ions will be attracted to the negative part of water molecules, while the negative chloride ions will be attracted to the positive part of water molecules (water is a polar molecule). That reaction is (by creationists’ definition) spontaneous. It is an inevitable outcome of the chemistry. No one has to sit there and will the molecules to interact with each other. They just do so automatically because of the way that charges, electrons, etc. behave. You might try to quibble over this example because it involved me (a conscious entity) dropping the salt into the water, but we can easily think of situations where the chemicals would meet without intervention (e.g., a cliff eroding into a lake).

This may seem straightforward so far, but it is critical to clarify that this definition of spontaneous must still apply even when we are talking about reactions that occur inside a living organism. Take photosynthesis, for example. Plants take in water (H2O) and carbon dioxide (CO2) and through a complex series of chemical reactions, they produce oxygen (O2) and glucose (C6H12O6). Various enzymes are involved, and the reaction is endothermic and requires energy from the sun. Thus, it is not spontaneous by the technical chemical definition, but it is spontaneous by the definition that creationists use when they say things like, “life can’t spontaneously arise.” In other words, it is an inevitable outcome of the chemistry in that environment. When you have those chemicals (including the various enzymes, etc.) plus an input of energy from the sun, the reaction will happen. No one has to force the individual atoms to interact.

Note: I will use this definition of spontaneous throughout.

Everything is nonliving matter

There is no such thing as living matter. The dichotomy between “living’ and “nonliving” matter is a completely false one that is perpetuated by the way that all of us (including scientists) talk, but it is a critical topic when it comes to abiogenesis, because creationists entire argument hinges on this false distinction between living and nonliving matter.

The problem here is that matter is never alive, but when it is arranged in certain ways, it results in chemical reactions that produce the property known as life. In other words, living organism are composed entirely of nonliving matter. You are, for example, predominantly composed of the elements oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus. These are nonliving atoms that come together to form nonliving molecules. When those molecules are arranged in a certain way, they chemically react and produce a living cell, and those living cells collectively from a living organism (you). You are alive, and your cells are alive, but the matter that makes those cells is not alive. It’s just a specific arrangement of nonliving atoms.

This may seem like an entirely pointless semantic quibble, but it is actual vital for this discussion, because, since matter itself is not alive, all life, by definition, arises from nonliving matter. When you make a sperm or an egg cell, for example, nonliving matter is simply being arranged into a living cell. Yes, that arrangement is being performed by living cells, but they are themselves just arrangements of nonliving matter, and they are simply providing the chemicals (aka nonliving matter) and environment necessary for spontaneous chemical reactions to arrange the chemicals into a living cell. The matter is never alive at any point in the process.

Now, I can already hear the objection that a living cell is required for that to happen. In other words, this argument states that even though the matter itself is not alive, a living organism is required to arrange the nonliving matter into a living cell. As I will explain in subsequent sections, however, there is absolutely no reason to think that assertion is true.

This is about chemistry, not consciousness

Before I go any further, I need to make a brief comment about consciousness, because someone will inevitably respond to my assertion that life is simply a product of complex chemistry by arguing that “chemistry can’t explain consciousness.”

I want to respond to that in several ways. First, prove it. You are a biochemical machine. You breathe in oxygen, which is transported to your cells thanks to haemoglobin in your blood. That oxygen, as well as glucose from your food, is then used for a complex chemical reaction known as cellular respiration. This produces the molecule ATP which can be reduced to ADP, resulting in a release of energy. That degradation of ATP to ADP powers your body. Every function of your body is controlled by chemistry and reducible to chemistry. Even when you are thinking, that is a result of chemistry in your brain (neurotransmitters, sodium ion channels, etc.). Given all of that, there is no good reason to think that consciousness is not also just a product of complex chemistry.

Having said that, however, this topic is actually completely irrelevant to the argument about abiogenesis, and I would really rather just drop it altogether. So, to that end, I will focus on bacteria from here on out. I don’t know anyone who thinks that bacteria are conscious, so we can talk about them from an entirely chemical perspective, even if you think that consciousness is more than chemistry. Further, the first cell is thought to have been something similar to a cyanobacteria, so talking about bacteria is rational path.

Bacterial reproduction

Diagram of a bacterium. Image credit: Ali Zifan via Wikimedia

Now that we have agreed to focus on bacteria, let’s talk about how bacteria reproduce. Bacteria are very simple organisms and really only consist of a few major parts: a cell wall (made of the chemical peptidoglycan), DNA, proteins known as ribosomes, cytoplasm (the gooey fluid inside), and a few other bits and pieces. Again, all of those parts are made of nonliving matter, and are themselves nonliving, but when they are arranged correctly, and the correct chemical reactions occur, the cell as a whole exhibits the properties that we use to define life. In other words, ribosomes are not alive, the cell wall is not alive, DNA is not alive, etc., but when all of those things are put together and the correct chemical reactions occur, we describe the entire cell as being alive. Further, we would describe it as “dead” only if those chemical reactions ceased. Thus, biological life is defined by the occurrence of specific chemical reactions.

When a bacterium detects that the environment and resources are good for reproducing, a series of chemical reactions are triggered. Most importantly, the contents of the cell (DNA, ribosomes, enzymes, etc.) are duplicated. The DNA duplication involves a series of enzymes and chemical reactions that read the DNA strands and make identical copies. Again, this is a spontaneous chemical reaction that will occur anytime that the right chemicals are supplied under the right conditions.

Unlike the DNA, the proteins are duplicated by the ribosomes (which are themselves made of proteins). The ribosomes are protein factories. They receive blueprints from the DNA (in the form of mRNA) and building materials from the rest of the cell (in the form of tRNA), and they arrange those building materials according to the blue prints. Here again, this all happens because of inevitable chemical reactions (given the reactants and environment; see note at the end for more details on how proteins are made).

Diagram of protein synthesis. Image credit: Kelvinsong via Wikimedia

Hopefully at this point the picture is becoming clear. The entire process of forming a new cell is just a long string of chemical reactions. It is true that in nature, we have only observed this entire chain of reactions occurring in living cells, but that is just because the cell provides the right environment, conditions, and reactants for those reactions to take place. If the right conditions occurred outside of a cell those reactions would still happen. Imagine, for example, that we figured out how to artificially produce ribosomes, then put them in a beaker with the correct reactants, mRNA templates, enzymes, tRNA, energy input, etc. Would they form proteins? Yes. In fact, we have done essentially that. We have developed methods known as cell-free protein synthesis that allow you to produce the proteins for a given strand of DNA in a test tube without needing a living cell!

The significance of PCR

For most of the history of life on planet earth, DNA replication only happened in one place: a living cell. During human history, DNA didn’t spontaneously replicate in nonliving environments. Just like the production of proteins and the other steps involved in making a new cell, DNA replication required a living cell. DNA replication is, however, just chemistry (just like the other steps of making a new cell), and scientists saw no reason why it shouldn’t be possible to replicate DNA if the right conditions were created outside of a cell. So, they began studying the chemistry, and after years of work, they figured it out, ultimately resulting in the polymerase change reaction (PCR).

If you ever take even an introductory course on genetics, you’ll almost certainly have to do a PCR reaction, because it is one of the most common tools in laboratories around the world (a substantial amount of my life has been spent running these reactions). To do PCR, you take a strand of DNA that you want to replicate, add the necessary chemicals (enzymes, bases, primers, etc.), put the mixture into a thermocycler that creates the correct temperature profile for the reaction to occur (i.e., the environment), and lo and behold, you replicate DNA without needing a living cell.

Why is that possible? Why is it possible to take a process that, in nature, requires a living cell, and do it without a living cell? Because the process is entirely chemical! Again, the cell just provides the environment necessary for that reaction to occur, but if you can replicate a suitable environment outside of a cell, then you can do the same reaction. Further, there is absolutely no reason to think that this only applies to DNA replication. Every step involved in making a cell is just a series of chemical reactions, and there is absolutely no reason why a living cell should be the only environment in which those reactions are possible.

Additionally, it is important to remember that the series of reactions that occur in living cells today are more complicated than would be necessary to form a rudimentary cell. Indeed, scientists are actively studying chemical reactions that can produce primitive versions of various cellular components without requiring a living cell.

Bringing it all together

Let’s recap, shall we? Matter itself is not living. Rather, when nonliving chemicals are arranged together and react in certain ways, they produce living organisms that consist of nonliving matter. Further, the processes and actions of these living organisms are simply the result of complex chemical reactions. Additionally, these chemical reactions occur “spontaneously” in that they will occur on their own given the right chemicals in the right environment. Indeed, all living organisms are accurately described as biochemical machines, with these “spontaneous” reactions driving their functions.

As a result of all of this, it is completely fair to say that life constantly arises from nonliving matter, because each new cell is formed by arranging nonliving matter into a configuration that will result in the chemical reactions that produce the properties that we describe as life. It is true that currently these reactions do not occur in nature outside of a cell. In other words, each new cell is formed by existing cells; however, because that formation process is entirely chemical, there is no reason to think that those chemical reactions could not occur elsewhere. To put that another way, living cells simply provide the right environment and resources for those reactions to occur, but if the right environment occurred outside of a cell, those reactions would still occur even in the absence of a cell. Indeed, we have clearly demonstrated this by replicating a key component of cellular reproduction (i.e., DNA replication) in the lab. Further, it is likely that the environment on planet earth billions of years ago would have also been conducive to these types of reactions.

In short, there is absolutely no reason to think that life couldn’t form “spontaneously from nonliving matter,” because matter is never alive, and the formation of life is nothing more than a complex series of chemical reactions.

Note: Someone is probably getting ready to point out that although PCR replicates DNA, it is not exactly the same reaction used by living cells. That is true, but completely irrelevant. There are lots of different variants of the DNA replication process found in nature, and it is entirely possible the first cells used mechanisms that were different from those of current cells. So, all that matters is that we were able to replicate DNA in the lab. In other words, the point is simply that a living cell is not required for that task to be accomplished. The end product is what matters, not the mechanism through which it happened.

More details on protein synthesis: The process here is complicated, but the simplest way to explain it is like this. DNA is a chemical molecule, and the four bases of DNA (ATCG) are four different chemical molecules. When the cell sends blue prints to the ribosome, it translates the DNA into mRNA, which also consists of four bases (AUCG; mRNA is a single-stranded complimentary copy of the DNA strand with T replaced with U). The bases on mRNA are arranged into sets of three, known as codons, and each codon codes for a specific amino acid. Once this strand of mRNA is in the ribosome, it will react with tRNA, which consists of anticodons attached to an amino acid. The anticodon is the compliment of the codon, and, because of the chemistry, anticodons (and, as a result, the amino acids they carry) are specific to specific codons. Thus, each anticodon reacts with a specific codon, ultimately resulting in its amino acid getting added to the amino acid from the previous anticodon. In other words, the ribosome matches the codons with the correct amino acid, resulting in reactions that bind the amino acids together into chains, and those chains fold to form proteins. I realize that may sound like the ribosome is a conscious entity that is consciously deciding how to do this, but it is not. All of this is 100% chemistry. In the presence of the right enzymes, chemical reactions will occur with the codons, anticodons, ribosome, amino acids, etc., ultimately causing the amino acids to string together in a certain order that is dictated by the chemistry of the RNA, which is in turn dictated by the chemistry of the DNA.

 Related post
Abiogenesis: An unsolved mystery is not evidence of a creator

Advertisements
This entry was posted in Science of Evolution and tagged , . Bookmark the permalink.

24 Responses to Life constantly arises from “nonliving matter”

  1. Kirk Durston says:

    “In short, there is absolutely no reason to think that life couldn’t form “spontaneously from nonliving matter,” because matter is never alive, and the formation of life is nothing more than a complex series of chemical reactions.” Well, there might be at least one reason …. if hundreds of scientists working on the problem for 50 years have thus far failed to demonstrate in the lab how it can be done, then that might be a reason for at least a wee bit of scepticism re. “there is absolutely no reason”. It doesn’t follow from this that it cannot be done, just that unbridled optimism is not yet justified.

    Like

    • Fallacy Man says:

      I disagree entirely. We are talking about an extremely complex set of reactions, and we have actually made a lot of advances in understanding the various components of it. The fact that scientists don’t have all the pieces together yet is not an indication or even suggestion that it is impossible.

      Like

  2. cosmicaug says:

    It is true that in nature, we have only observed this entire chain of reactions occurring in living cells, but that is just because the cell provides the right environment, conditions, and reactants for those reactions to take place. If the right conditions occurred outside of a cell those reactions would still happen. Imagine, for example, that we figured out how to artificially produce ribosomes, then put them in a beaker with the correct reactants, mRNA templates, enzymes, tRNA, energy input, etc. Would they form proteins? Yes. There is no reason to think that they wouldn’t because, again, it’s just a series of chemical reactions. The living cell is irrelevant to the process, other than that it provides the environment and resources.

    I’m not sure what you intend with this requirement for artificially produced ribosomes (forgive me for saying that I find it to be an artificial requirement) and what you mean by artificial. In any case, there’s nothing hypothetical about it. If all the components are in place, it will simply work: just add water (as well as template DNA or RNA) and you will get production of the coded protein! You can buy cell free expression kits where a biotech company has done all the hard work for you (purifying the required components from E. coli) and, apparently, being able to do this has its uses in research settings. Though PCR uses a highly artificial non isothermal process to work properly[1] (and though cell free synthesis has many more moving parts, so to speak), for purposes of this blog post, cell free protein synthesis is still analogous to PCR in that you are recreating one highly complex fundamental life process in the laboratory within a context that no reasonable, knowledgeable person would consider to represent life.

    1· The temperature cycling is fundamental to the way PCR works and not something that you see in nature (as far as I know). However, even this is not necessary for effective artificial amplification of nucleic acid sequences. You can also do the same sort of thing that PCR does by providing, with your DNA template, very highly artificial primer sequences to your DNA polymerase such that it will result in a looping amplification that happens in a more “natural”[2], isothermal way. This is referred to as LAMP (loop mediated isothermal amplification).
    2· I’m sure someone might argue that such looping is also “unnatural” but then we might be forced to argue that other non-standard ways of DNA replication, such as rolling circle in some viruses, are similarly unnatural. In any case, as Fallacy Man points out, whether we are exactly replicating a natural process or not is beside the point.

    Liked by 1 person

    • Fallacy Man says:

      Thank you for your comment. You are correct about all your points and I should have include CFPS in my original post. I have now added a few lines about it to correct that situation.

      Like

  3. boammaaruri says:

    The properties of living matter are irreducible to chemical properties. Reductionism in biology has been demonstrated philosophically to be untenable. Michael Polanyi wrote an excellent article in Chemical Engineering News and the journal Science about 50 years ago on this topic. (http://www.informationphilosopher.com/solutions/scientists/polanyi/Polanyi_Life_Structures.pdf).
    Below is my own illustration of the proposition that the chemical facts of DNA do not determine the symbolic and semantic facts of DNA.
    Imagine giving a DNA strand such as (CGCAGC) to a biochemist who knows all about the genetic code and asking them to tell you which amino acids are represented by the DNA strand. The problem is they could give you all of the physiochemical properties about the DNA strand such as its molecular weight, bond angles and bond lengths, type of bonds, activation energy to break the bonds however when it came to telling you which amino acids are represented by the DNA strand there are a number of possible interpretations all equally possible but mutually exclusive.
    First interpretation could be [CGC] is Arginine and [AGC] is Serine. Second interpretation could be the strand is broken in between a codon and that C[GCA]GC only represents one amino acid. Therefore in this case GCA is Alanine. Third interpretation could be the strand contains one codon starting from the third nucleotide CG[CAG]C and in this case (CAG) is Glutamine.
    There are other interpretations possible such as the codon should be read backwards instead. Perhaps the strand does not represent any amino acids because it was created from scratch in a lab rather than being taken from an organism. One could argue that of course the context is required to understand the meaning of it – but then that is precisely the point that things such as context, representation and interpretation do not apply to chemical properties and laws. The main point is that the physical facts are indeterminate with regards to the information content. There are a number of different possible interpretations of what the nucleotides represent even though in all possible interpretations the chemical and physical properties, as well as the molecules involved are exactly the same. This demonstrates that the symbolic representation of amino acids by nucleotides is not identical and is not determined by the chemical and physical properties of the chemicals.

    Like

    • Fallacy Man says:

      That is utter nonsense. Context is absolutely 100% vital. When a ribosome reacts with a strand of mRNA, it doesn’t do so with only a few isolated bases. The reactions involve the entire strand, which includes bits that dictate the order of the strand, where to start the processes, etc. You can’t just rip out a single part of a reaction and say, “well we can’t understand the whole process form this one tiny bit, so the whole process must not be reducible to chemistry.”

      Now, yes, sometimes a mutation occurs resulting in the loss of a base, frame shift, etc., but when that happens the codons still code for specific amino acids, they just aren’t the ones that were supposed to be being made. For example, you said, “Second interpretation could be the strand is broken in between a codon and that C[GCA]GC only represents one amino acid. Therefore in this case GCA is Alanine. ” That is, however, completely incorrect. CGC is Arginine and AGC is Serine. Maybe that is not what the cell was trying to make, but that is what the codons currently code for. That is the information that they convey.

      Let me try this example, consider the word “there.” By your argument, we don’t actually know if the word is “there” or “the” with an extra “er,” or “therefore” without the “fore,” etc. That’s an absurd argument though. The word is “there.” Maybe that is not what the word was supposed to be, maybe I made a typo, but that is what the word is. Even so, if you show the strand CGCAGC to any biochemist anywhere in the world, they will correctly say that it codes for Arginine and Serine. Maybe that is not what it was supposed to code for, and if you add a different base to the front, invert it, remove a base, etc. the code will change, but Arginine and Serine is the meaning of those 6 bases in isolation. The fact that it means something else if you change it or put it into a different context is totally irrelevant.

      Honestly, I’m not even sure what you are trying to argue here. Are you suggesting the strands of DNA (and subsequent mRNA) are not sufficient for dictating the code of a protein? That would be quite a surprise to every biologist in the world (note: epigenetics can influence the expression of genes, but that is an entirely different issue).

      Like

    • Fallacy Man says:

      Let me ask this, because it’s really not clear to me what you are arguing. Do you agree that I can take a stand of DNA for a protein that I’m interested in, use a cell-free protein synthesis kit, and produce the protein that I was after using only the chemistry of that kit and the DNA strand?

      If you agree, then what on earth is your argument?

      If you disagree, then you are clearly wrong, because this is a well-established technique.

      Like

      • boammaaruri says:

        I agree – you can make a protein using a cell-free protein synthesis kit with a DNA strand. The biomechanics of the process are not in question (although one could argue as Polanyi does that biochemical machines are irreducible to chemical laws – but that is an argument for another day). To use an analogy. The meaning of a word in a book is not determined by the physical properties of the ink and paper. The fact that you can make a copy of that book with all its words using a physical photo-copying machine does nothing to change the fact that the meaning of words is not determined by and reducible to chemical laws such as covalent bonds and bond angles. Similarly the fact that a set of nucleotides represents another molecule (an amino acid in this case) is not a chemical property but a semantic property. No one disputes that the chemistry is necessary for protein synthesis from DNA, anymore than anyone denies that creating a book made from paper and ink is a physical process.

        Like

        • Fallacy Man says:

          Then what are you arguing? If the chemistry alone is all that is necessary to make a protein, then, by definition, the protein is reducible to the chemistry, because nothing else is required.

          With your ink example, you seem to be after some metaphysical “meaning,” but that is irrelevant here. The chemistry only “means” something in that it provides the code for making a cell (and that code will be automatically acted upon by the other chemicals).

          Let me ask this, do you agree that a cell is formed using nothing but chemistry?

          Like

          • boammaaruri says:

            The surface tension of a liquid is a property reducible to the chemical properties of its constituents even though an individual molecule cannot by itself have surface tension. Surface tension is explained by the intermolecular forces between molecules. It is therefore determined and explained by the chemical properties and interactions of the individual molecules.
            Please explain to me how the covalent bonds between the different atoms explain the emergence of a “code”

            The claim in the analogy is relatively simple – it is that the meaning of a word in a book is not determined by the physical properties of the ink in which it is written. You cannot explain the semantics of the word as arising from the properties of the ink in which it is written. This is a fact -whatever one may think about the nature of the mind.

            The metaphysical distinction I’m trying to get at is the difference between matter and form. An ice sculpture is made out of nothing but water – but the material properties of the water alone are not sufficient for determine the form of the sculpture. The same material components could take on different forms and therefore the material components again indeterminate with regards to the form of the sculpture. The components of a cell are molecules but they do not explain the form/structure / organization of the cell.

            Like

            • Fallacy Man says:

              “The components of a cell are molecules but they do not explain the form/structure / organization of the cell.” I completely disagree with you on this.

              A given strand of DNA will only form a given protein because of the chemical reactions. Each codon only reacts chemically with specific anticodons. That’s why the “code” works, because each base in the code only reacts chemically with certain other bases. Again, I don’t understand your argument, because you seem to acknowledge this. I just don’t understand how you are simultaneously saying that a strand of DNA can, entirely though chemistry, form a specific protein, but somehow that protein isn’t reducible to chemistry. That makes no sense.

              I agree with you that an ice sculpture is not reducible to chemistry, but that is an entirely different situation. It wasn’t formed by running a series of chemical reactions that will inevitably form that particular sculpture. In contrast, a cell is formed by a series of chemical reactions that will inevitably form that particular cell. The two aren’t analogous. To put that another way, there is nothing in the chemistry of water that dictates that it will form that particular shape. In contrast, the shape, function, etc. of a cell is absolutely dictated by the chemistry because, again, each codon only reacts chemically with specific anti-codons, causing them to string together to form specific proteins that perform specific functions, all of which is entirely dictated by chemistry. If it wasn’t dictated by the chemistry, then we wouldn’t be able to reproduce it in the lab, but we can, ergo it’s the chemistry.

              I reiterate that if chemistry is all that is need to form a cell (or even just a protein), then, by definition, that cell (or protein) is reducible to the chemistry.

              Like

            • Fallacy Man says:

              Your book analogy is similarly specious. The words themselves don’t do anything because they aren’t chemical machines. In contrast, a cell (or protein is). So yeah, I agree that a word’s function is not dictated by the chemistry of the ink, but that is totally irrelevant because a printed word is not even remotely analogous to a cell (or component of a cell). If the word operated by reacting chemically with other words, then it would be analogous, but, importantly, at that point it would in fact be reducible to the chemistry. In other words, if each word consisted of a particular chemical structure and formed sentences by reacting chemically with other words, then the book would be reducible to chemistry. Indeed, that is exactly how cells work.

              Like

    • cosmicaug says:

      boammaaruri writes:

      The properties of living matter are irreducible to chemical properties. Reductionism in biology has been demonstrated philosophically to be untenable. Michael Polanyi wrote an excellent article in Chemical Engineering News and the journal Science about 50 years ago on this topic. (http://www.informationphilosopher.com/solutions/scientists/polanyi/Polanyi_Life_Structures.pdf).

      Below is my own illustration of the proposition that the chemical facts of DNA do not determine the symbolic and semantic facts of DNA.

      Imagine giving a DNA strand such as (CGCAGC) to a biochemist who knows all about the genetic code and asking them to tell you which amino acids are represented by the DNA strand. The problem is they could give you all of the physiochemical properties about the DNA strand such as its molecular weight, bond angles and bond lengths, type of bonds, activation energy to break the bonds however when it came to telling you which amino acids are represented by the DNA strand there are a number of possible interpretations all equally possible but mutually exclusive.

      First interpretation could be [CGC] is Arginine and…

      With your example, you appear to be refuting something proposed by no one. I would say that the issues of context are actually much more extreme than what you are illustrating. However, that is all they are, issues of biochemical context. For, as you mention, [CGC] to code for Arginine and for [AGC] to code for Serine, in a real sense, you need for that sequence of two codons to be preceded by a start codon in the proper reading frame and also by an RNA polymerase binding site and, for proper expression, and a ribosome binding site as well. Without that it becomes just a polynucleotide of no particular significance. In addition you will need ribosomes and you will need an RNA polymerase and you may need, depending on the particular context, assorted transcription factors (plus many other things such as, proper pH & temperature, proper cations, loaded amynoacyl RNAs, etc.).

      But it goes beyond that. You mention the fact that this sequence can be interpreted according to six possible reading frames and give examples (again, none of them will be expressed if the preconditions I mention are met —indeed, depending on context, the sequence may mean nothing at all, may be part of a larger sequence having a regulatory function or may code for an RNA that is not a mRNA). One of the reading frames would be to look at CG[CAG]C in a backwards frame and this corresponds to the [CTG] codon. CTG is leucine in the standard codon table but it can sometimes be a start codon and then it’s methionine. It is also threonine in the yeast mitochondrial code (table 3) and serine in the alternative yeast nuclear code (table 12) unless it is being read as a start, in which case it becomes a methionine. Or for table 26 it’s an alanine unless it is being used as a start in which case it becomes methionine. That is, that one three nucleotide sequence, read as a codon in a single direction, can code for five different amino acids depending on the context in which it is found (and this is assuming that this context is happening within known biology —but other contexts are undoubtedly possible).

      What I would questions would be the notion that because we need to have proper biochemical context to see a given chemistry or process in living systems (for instance, it is not difficult to imagine alternative contexts where a given nucleotide sequence codes for even alternative amino acids that are not part of normal ribosomal synthesis —and, indeed, some researchers are working on exactly that) it somehow implies that the processes that we call life are somehow not reducible to the laws of chemistry of non-living things. No meaningful differentiation between the two exists. The former is what we call it when we discern certain emergent properties in the latter. If on the other hand, all that you mean to say that DNA is not computer code, I have no disagreement with you.

      Liked by 1 person

  4. angel199978745 says:

    It should also be noted that we can, in fact, use a cell free system to produce proteins as well as DNA. In much the same way that we can create the environment necessary to cause DNA replication, we can also use cell components to perform translation in a test tube.

    https://www.ncbi.nlm.nih.gov/pubmed/24395424

    Like

  5. Fallacy Man says:

    All comments sections close 1 month after posting an article because otherwise the mountain of comments grows endlessly and I don’t have time to deal with them.

    Also, if you read the comment rules, they specifically require that all posts be on topic, and dictate that any posts that are not on topic will be removed.

    PS, I have not had time to read your entire comment since it is quite long, nor will I be debating it for the reasons outlined above, but from quickly looking over the first bit, your argument seems to be little more than semantics. I don’t care if you want to say that the heat is “trapped,” “stored,” etc. The point remains the CO2 makes it more difficult for IR to leave the earth, resulting in more energy being at least temporarily stored in the atmosphere, and we know that this has a big affect on the climate. Use whatever words you want, the point of the premise stands (it was deliberately written in a way that the general public would understand it).

    Like

  6. jcznk says:

    So basically we could summarize your argument this way:

    0) creationists think that life can’t derive from non-living matter (they say “it cannot arise spontaneously”)

    –> let’s prove them wrong

    1) you point out that there’s no substantial difference between living and non-living matter, the only difference is the system they belong to/the cascade of reactions they take part in

    1.1) you make some examples of non-living matter becoming part of a living system
    (reproduction of cells or organisms)

    –> checkmate, creationists

    Your argument would be right only if the point you’re trying to prove wrong was: “life can’t arise spontaneously because there’s a strict difference between living and non-living matter”.

    I don’t doubt that some creationists might believe something like that is right, but that’s a pretty silly argument many would disagree with.

    A slightly more educated creationist could argue that “life cannot arise spontaneously from non-living matter because it seems extremely unlikely, to the point of being impossible, that a completely random sequence of physical/biochemical reactions could ever bring to the creation of a system as complex and fine-tuned as life (even in it’s most basic, unicellular forms). You therefore either need an intelligent designer or a pre-existing living being to create life from non-living matter”.

    I’m not a creationist, I’m just saying that unless I missed something yours appears to be a pretty weak argument.

    TL DR: pointing out that there’s no substantial difference between living and non-living matter does not prove much, if anything.

    Like

    • Fallacy Man says:

      Those are two separate arguments. The statement, “life can’t arise spontaneously because there’s a strict difference between living and non-living matter” is nearly word for word what I have had many creationists tell me in person and in the comments on this blog/facebook page. Not all of them use that argument, but a great many do.

      Like

      • jcznk says:

        I see ^^ I wonder how do these people think eating works xD
        I also guess I may have gone through your reasoning too hastily, I’ll now give it a second try.

        Like

  7. jcznk says:

    Over simplifying a little less: saying “that the same processes happening inside cells don’t strictly need a living system to take place” doesn’t prove much.

    You should first bring evidence that such complex patterns of reactions can happen “spontaneously”.

    PCR is not a good example not because “there isn’t actually any process like that in living systems” but because it’s an artificial technology created by an intelligent designer aka the human species.

    Like

    • cosmicaug says:

      jcznk writes:

      So basically we could summarize your argument this way:

      0) creationists think that life can’t derive from non-living matter (they say “it cannot arise spontaneously”)

      –> let’s prove them wrong

      1) you point out that there’s no substantial difference between living and non-living matter, the only difference is the system they belong to/the cascade of reactions they take part in

      1.1) you make some examples of non-living matter becoming part of a living system
      (reproduction of cells or organisms)

      –> checkmate, creationists

      What we have here, essentially, is an argument against vitalism. I’d like to think that vitalism is dead (even with creationists) but I think you might find that it is more prevalent than you think.

      jcznk writes:

      PCR is not a good example not because “there isn’t actually any process like that in living systems” but because it’s an artificial technology created by an intelligent designer aka the human species.

      Almost the entirety of molecular biology tools that we use are naturally occurring (I won’t say the entirety because often we make modifications). PCR is no different. There are differences in the process. The natural system is more complex. The “artificial” system makes normal the DNA replication cycle happen around an end sequence delimited section of DNA happen by supplying primers that match those end sequences and by using temperature to separate DNA strands (when we repeat this we get the “chain reaction” part of the process to happen). The natural counterpart of this process does not do the “chain reaction”, strand separation of the DNA is achieved by enzymatic means (enzymes we call helicases) and, instead of having primers supplied by a biotechnology company, primers are created in place by special enzymes (enzymes we call primases).

      So while there isn’t exactly a process exactly like PCR in nature, the technique we call PCR adapts processes that happen naturally in order that they may be used to serve our ends. Viruses do this as well (they are just better at it than we are).

      Like

    • Fallacy Man says:

      “You should first bring evidence that such complex patterns of reactions can happen ‘spontaneously'” I think I did that. Photosynthesis, protein synthesis, DNA replication, etc. are all examples of extremely complex reactions that happen spontaneously.

      Like

      • jcznk says:

        But am I missing something or don’t these processes need some sort of pre-existing biological machinery in order to take place?

        I’ll now read again and more carefully your text.

        Like

        • Fallacy Man says:

          They currently occur inside living cells, but the living cells are simply providing the correct environment for those reactions to occur. Since they are entirely chemical processes, there is no reason why they could not occur if the right environment occurred outside of a cell.

          Like

Comments are closed.